Class PosParser

  • All Implemented Interfaces:
    Iterator<picard.illumina.parser.PositionalData>

    public class PosParser
    extends PerTileParser<picard.illumina.parser.PositionalData>
    PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs). This parser takes a map from tilesToFiles and a FileType enum value indicating whether or not these are POS,LOCS, or CLOCS files. The only client classes to this class should be IlluminaDataProvider and test classes. Check out AbstractIlluminaFileReader, PosFileReader, LocsFileReader, and ClocsFileReader for more information on Position related illumina files.
    • Method Detail

      • makeTileIterator

        protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData> makeTileIterator​(File file)
        Make an CloseableIterator based on the given file and fileType specified at construction. This method wraps a reader in an iterator that converts it's output to the output format expected by IlluminaDataProvider (PositionalData).
        Specified by:
        makeTileIterator in class PerTileParser<picard.illumina.parser.PositionalData>
        Parameters:
        file - A file for the current tile being parsed
        Returns:
        An iterator over the PositionalData in that file.